Yes, but eating *some* bacteria isn’t what hurts you. Your stomach handles bacteria every day, surfaces are covered with them. However, when bacteria and fungi have been growing for a while on food, they’ve eaten some of it and, well, pooped. The toxins they release after they eat are designed to kill things, like other microbes looking to “share” the food that the current diners have found.
Penicillin is the poop of the Penicillium chrysogenum ~~bacteria~~ fungus, released to keep others from sharing the bread P.C. is living on. (Fun bonus fact, a relatives Penicillium roqueforti and Penicillium camemberti are used because we like the flavor their poop gives cheese.)
Enough microwaves to destroy these toxin molecules would virtually incinerate your food.
Edit: microbe type, oops
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